#Set up

#s1
rm(list=ls())

setwd ("C:/Users/cecidy/Google Drive/ZH_analysis/")

source("ZHfunctions.R")
options(scipen=9999)

ZeroHunger <- read.csv("Data/ZHdf/ZeroHungerDF_2020.csv",header=TRUE, sep=",")

#s2
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#start1_

#ZH and Protein robustness sample

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#1. Prepare each dataframe

#Get Rural municipalities, dont include those very large municipalities
Poverty04 <- subset(ZeroHunger, PopDensity20042004Analysis<=150 & SizeKm22004Analysis<=10000)

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#Get list of vars
load(file = "Data/ForSamples/MPI00list.rda")
load(file = "Data/ForSamples/Basic04.rda")

RuralPoverty04 <- subset(Poverty04, select=c("ZHPerCapTotal04to13for2004Analysis1000",Basic04,
                                             "TotalKcal2013percapperday","TotalgramProtein2013percapperday",MPI00List))
RuralPoverty04 <- na.omit(RuralPoverty04)

#Then take away the ones affected by rural credit
load(file = "Data/ForSamples/EcludeForRCProb04.rda")

RuralPoverty04 <- subset(RuralPoverty04,(!(IBGECode7digit %in% EcludeForRCProb04)))

#Then take away those that have boundary change 2000-2004
Mun00analysis <- read.csv("Data/ForSamples/ListMunicipalitiesChanged00to10Analysis.csv",header=TRUE, sep=",")
TakeOUt <- c("2005","2009")#I dont need those - those are already dealt with in the 2004 data!

Mun00analysis <- subset(Mun00analysis, (!(YearOfCreation %in% TakeOUt)))
mun00list <- as.vector(Mun00analysis$IBGECode7digit)

RuralPoverty04 <- subset(RuralPoverty04,(!(IBGECode7digit %in% mun00list)))

#Just copy to get the "quality" dataset
RuralPoverty04quality <- RuralPoverty04

#Make logged variables

#First make MPI with the correct 0s
test <- NrOfZeroALL(RuralPoverty04quality)#This gives me all the vars with 0s
MPIadd <- test[[1]]
Otheradd <- test[[2]]

#For the MPI because Ive not previously renamed when adding I just override the vars with 0 with the minimum/2
WithAdded <- lapply(MPIadd,function(y) AddConstant(RuralPoverty04quality,y,addName=""))
WithAdded <- data.frame(do.call("cbind",WithAdded))

RuralPoverty04quality[,MPIadd] <- WithAdded[,MPIadd]#just override

#Then I need to make the MPI - here I need to use the 00 function
RuralPoverty04quality <- MakeMPI00(RuralPoverty04quality)

#Then for the others I cbind them on, and because Ive not included any of previous noCero there no duplicates
RuralPoverty04quality <- cbind(RuralPoverty04quality,lapply(Otheradd,function(y) AddConstant(RuralPoverty04quality,y,addName="nocero")))#

#################################################################################################

#And finally I need to log variables - get a list of all names

OtheraddCero <- paste(Otheradd,"nocero",sep="")#here which are names no cero

cols.log <- c("ZHPerCapTotal04to13for2004Analysis1000","MPI2000for2000Analysis","MPI2010for2000Analysis",
              "GDPPerCapPublicrealN2004for2004Analysis1000",OtheraddCero,"RemoteMinPopFifty2004Analysis",
              "MeanElevationfor2004analysis","MeanSlopefor2004analysis",
              "PopDensity20042004Analysis","SizeKm22004Analysis")
addlog <- function(x) log10(x)
Log10variables <- data.frame(sapply(RuralPoverty04quality[cols.log],addlog))
colnames(Log10variables) <- paste(colnames(Log10variables), "log10",sep="")

#Get all onto ZH
RuralPoverty04quality <- cbind(RuralPoverty04quality,Log10variables)
head(RuralPoverty04quality)

##########################################################################################################################

#Remove those I dont need
Log10variables <- NULL
Poverty04 <- NULL
ZeroHunger <- NULL
TempVars <- NULL
WithAdded <- NULL

#####################################################################

#Make scaled and logged ZH variables, and set contrasts (obs contrast is also set afresh in analysis script)
RuralPoverty04quality<- getDataFrame(RuralPoverty04quality,"contr.Sum",
                                     contrastVar1="stateName",contrastVar2="Biomefor2004Analysis",setRefToMostCommonLevel,
                                     BaseVar="ZHPerCapTotal04to13for2004Analysis1000log10",
                                     MainName="ZHPerCapTotal04to13for2004Analysis1000log10scaledMain")

#fin1_
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#start2_

#Prepare vectors of variables for regressions

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Depvar <- "TotalgramProtein2013percapperdaynocerolog10"

IndepVarLin <- "ZHPerCapTotal04to13for2004Analysis1000log10scaledMain"#already scaled so dont need to do it again

baselineDepVar <- "scale(TotalgramProtein2004percapperdaynocerolog10)"

stateName <- "stateName"

intLin <- c("ZHPerCapTotal04to13for2004Analysis1000log10scaledMain","stateName")
intLin <- paste(intLin,collapse="*")

#For CBPS models
cbpsDepVar <- "ZHPerCapTotal04to13for2004Analysis1000log10"
cbpsbaselineDepVar <- "TotalgramProtein2004percapperdaynocerolog10"

#########################################################################################################################
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#For MPI00 run this aswell to update to the correct one!

xvars <- c("scale(MPI2000for2000Analysis)","scale(GDPPerCapPublicrealN2004for2004Analysis1000log10)",
           "scale(TotalHectareCrops2004for2004Analysisnocerolog10)","scale(TotalHectarePasture2006for2004Analysisnocerolog10)",
           "scale(TotalHectareFarmsLess502006for2004Analysisnocerolog10)","scale(RemoteMinPopFifty2004Analysislog10)",
           "scale(ChangeCummulativeSPEI02and04to11and13for2004Analysis)","scale(TotRCpcNOPRONAF04to13for2004Analysis1000nocerolog10)",
           "scale(MeanElevationfor2004analysislog10)","scale(MeanSlopefor2004analysislog10)",
           "scale(PopDensity20042004Analysis)","scale(SizeKm22004Analysis)",
           "Biomefor2004Analysis")

cbpsVars <- c("MPI2000for2000Analysis","GDPPerCapPublicrealN2004for2004Analysis1000log10",
              "TotalHectareCrops2004for2004Analysisnocerolog10","TotalHectarePasture2006for2004Analysisnocerolog10",
              "TotalHectareFarmsLess502006for2004Analysisnocerolog10","RemoteMinPopFifty2004Analysislog10",
              "ChangeCummulativeSPEI02and04to11and13for2004Analysis","TotRCpcNOPRONAF04to13for2004Analysis1000nocerolog10",
              "MeanElevationfor2004analysislog10","MeanSlopefor2004analysislog10",
              "PopDensity20042004Analysis","SizeKm22004Analysis","stateName","Biomefor2004Analysis")

##################################################################################################

#fin2_
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